If you search for "configure automatic updates gnome" (without the quotes), the third result will be from help.gnome.org, which you'd think might be useful, but isn't. The Gnome Help site is rubbish, not by virtue of being badly written or designed, but by virtue of being thirteen years out of date. It refers to Gnome 2 (does anybody use Gnome 2 in 2021) and is not relevant today.
The Gnome Blog states that Gnome allows the automatic installation of updates, with configuration options in Gnome Software for installation and notification of installation, for but this turns out to be for Flatpacks only.
So here is a quick guide to configuring automatic updates in Gnome - in this case on Debian Buster.
The Gnome Help page refers to PackageKit being updated by a cron-job. (PackageKit being an update system that works in different distributions and cron being a job-scheduler.)
This was true in 2007, but today it's the Systemd scheduler that triggers updates, as I wrote about here. In XFCE this is not enabled by default, but in Gnome it is, because the package unattended-upgrades is installed, which sets a configuration file which tells APT (the Debian package manager) to check for updates and automatically install security updates when it is triggered by the Systemd timer.
Configuration is done via launching Software & Updates, or Synaptic > Settings > Repositories (it's the same window).
We can confirm that configuration settings are set in the unattended-upgrades configuration file 20auto-upgrades by watching it as we change the check interval.
If you look in that folder you will also notice a file called 20packagekit, which is there to make sure PackageKit knows about updates too.
I presume it is still PackageKit that Gnome Software uses to notify you of available updates. I will have to leave that for another investigation. I don't use Gnome Software because it always asks to restart the computer to install updates even through this is not necessary. Maybe it's possible to configure that too.
For now, I hope this post is useful to somebody like me who has observed updates in Gnome 3 and wondered what was happening.
[Edited for accuracy and clarity.]
[Corrected to reflect the fact that Unattended Upgrades actually installs all packages by default in Debian Buster and later.
The default setting for Unattended Upgrades was changed in Buster. The previous default was to apply security updates, but the default now is to update all packages.
I found a note in the "News" file (found in /usr/share/doc/unattended-upgrades) which states:
Unattended-upgrades in previous versions defaulted to install security updates only on Debian by using the label=Debian-Security origin pattern. Now it is changed to allow updates with label=Debian, which allows applying stable updates in stable releases and following all package updates in testing and unstable.
In stable releases this unlocks installation of security updates depending on package versions present only in stable updates.]
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